Formalin-fixed paraffin-embedded (FFPE) tissue samples constitute a vast panel of pathologically well-characterised clinical specimens and these histological sections represent a huge resource that can be used to conduct biomarker research into various diseases. However, purification of quality, amplifiable RNA from formalin-fixed, paraffin-embedded (FFPE) tissue can be a challenging task. The fixation process can be extremely aggressive and can result in fragmentation of the nucleic acids present in the sample. Fixation also introduces cross-linking which can hamper the processing capability of many downstream applications. The storage conditions of FFPE samples can also play a role in the quality of the DNA present in the sample. Archived FFPE tissue blocks and slides may be decades old and have been subjected to conditions that have compromised the integrity of the sample.

Formalin-fixed tissue samples are therefore a challenge for DNA extraction, often leading to low yields of amplifiable DNA and poor performance in subsequent steps involving enzymatic manipulation, including reverse transcription and sequencing library preparation. However, there are reagents optimised for DNA extraction from such samples.